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Open data
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Basic information
Entry | Database: PDB / ID: 7vud | ||||||
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Title | Carotenoid Cleavage Dioxygenase 1 from Osmanthus fragrans | ||||||
![]() | Carotenoid cleavage dioxygenase 1 | ||||||
![]() | PLANT PROTEIN / Carotenoid Cleavage Dioxygenase 1 (CCD1) / lycopene / ionone / psi-ionone / pseudo-ionone. | ||||||
Function / homology | Carotenoid oxygenase / Retinal pigment epithelial membrane protein / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / metal ion binding / NICKEL (II) ION / Carotenoid cleavage dioxygenase 1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, D. / Xue, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Carotenoid Cleavage Dioxygenase 1 from Osmanthus fragrans Authors: Sharma, D. / Xue, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.7 KB | Display | ![]() |
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PDB format | ![]() | 174.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3npeS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 63356.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: D4QE74 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.09 Å3/Da / Density % sol: 79.79 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M Tris pH 7.5, 1.5M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 98.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→49.53 Å / Num. obs: 39479 / % possible obs: 100 % / Redundancy: 81 % / CC1/2: 0.996 / Rmerge(I) obs: 0.0148 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.8→2.91 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4387 / CC1/2: 0.38 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3npe Resolution: 2.8→49.48 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.469 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / ESU R: 0.303 / ESU R Free: 0.251 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.231 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→49.48 Å
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Refine LS restraints |
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LS refinement shell |
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